Following allogeneic marrow transplantation a competent marrow microenvironment consists of a complex mixture of both donor and host derived cells. Clearly some forms of genetic disparity between donor and host can compromise appropriate interactions and function of these cells. The competency of the microenvironment can also be compromised by viral infections, and the underlying disease process as in rare cases of aplastic anemia. As we come to precisely define each component of the microenvironment, it will become possible to accurately diagnose causes of poor marrow function and develop methods for prevention and treatment.